List of Figures

Chapter 1: Modeling the Activity of Single Genes

Figure 1.1: Processes involved in gene regulation: (1) transcription factor binding, (2) formation of transcriptional complex, (3) RNA polymerase binding, and (4) transcription initiation.
Figure 1.2: Eukaryotic DNA consists of exons and introns. Exons code for proteins, introns are spliced out of the mRNA. Alternative splicings are possible.
Figure 1.3: Translation consists of a ribosome moving along the mRNA one codon (three bases) at a time and translating each codon of the mRNA into an amino acid of the final protein.
Figure 1.4: Transcriptional regulation at a specific gene (asg) operator in budding yeast, for ? and a/ ? cells. Note multiple protein protein and protein DNA interactions in a complex leading to activation of the transcriptional apparatus. DNA is at the bottom and includes the asg operator. Redrawn from Johnson (1995).
Figure 1.5: Some transcription factors act at certain times, some in certain cells, and others in response to signals.
Figure 1.6: Kinetic model of two proteins, P and Q, binding to DNA.
Figure 1.7: Finite-state machine for the Boolean network example in the text.
Figure 1.8: Finite-state machine for the kinetic logic example in the text.

Figure 2.1: The life cycle of ? phage. A phage injects its DNA into the E. coli host, then either (left) replicates and destroys the host cell lysis or (right) integrates its DNA into the host DNA lysogeny.
Figure 2.2: A...

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